Sparsification of RNA structure prediction including pseudoknots

31.12.2010

Möhl M, Salari R, Will S, Backofen R, Sahinalp SC

Algorithms Mol Biol. 5(1):39

Algorithms Mol Biol       online article

We introduce sparsification to significantly speedup the dynamic programming approaches for pseudoknotted RNA structure prediction and also lower the space requirements.
We provide the first application of sparsification to pseudoknotted RNA structure prediction specifically and to handling gapped fragments more generally - which has a much more complex recursive structure than other problems that have been sparsified before.